Package | Description |
---|---|
com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
|
com.compomics.util.experiment.identification.protein_inference |
Classes related to protein inference.
|
com.compomics.util.experiment.identification.protein_inference.fm_index |
Protein sequence database indexing classes based on Burrows-Wheeler transform.
|
com.compomics.util.experiment.identification.protein_inference.proteintree |
Protein sequence database indexing classes.
|
Modifier and Type | Method and Description |
---|---|
SpectrumMatch |
SpectrumMatch.getPeptidesFromTags(ProteinTree proteinTree,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance,
boolean scoreInAscendingOrder,
boolean ascendingScore)
Creates a peptide based spectrum match where peptide assumptions are
deduced from tag assumptions.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<PeptideProteinMapping> |
PeptideMapper.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the protein mappings for the given peptide sequence.
|
ArrayList<PeptideProteinMapping> |
PeptideMapper.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance)
Returns the protein mappings for the given peptide sequence.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences)
Mapping tags against the proteome.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance)
Mapping tags against the proteome.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithoutVariants(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
int indexPart)
Mapping tags against proteome without variants.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithVariants(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
int indexPart)
Mapping tags against proteome with variants.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<PeptideProteinMapping> |
ProteinTree.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences) |
ArrayList<PeptideProteinMapping> |
ProteinTree.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance) |
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